In a complex disease such as tuberculosis, the evidence for the disease and its evolution may be present in multiple modalities such as clinical, genomic, or imaging data. Effective patient-tailored outcome prediction and therapeutic guidance will require fusing evidence from these modalities. Such multimodal fusion is difficult since the evidence for the disease may not be uniform across all modalities, not all modality features may be relevant, or not all modalities may be present for all patients. All these nuances make simple methods of early, late, or intermediate fusion of features inadequate for outcome prediction. In this paper, we present a novel fusion framework using multiplexed graphs and derive a new graph neural network for learning from such graphs. Specifically, the framework allows modalities to be represented through their targeted encodings, and models their relationship explicitly via multiplexed graphs derived from salient features in a combined latent space. We present results that show that our proposed method outperforms state-of-the-art methods of fusing modalities for multi-outcome prediction on a large Tuberculosis (TB) dataset.
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Graph neural networks (GNNs) are widely used for modeling complex interactions between entities represented as vertices of a graph. Despite recent efforts to theoretically analyze the expressive power of GNNs, a formal characterization of their ability to model interactions is lacking. The current paper aims to address this gap. Formalizing strength of interactions through an established measure known as separation rank, we quantify the ability of certain GNNs to model interaction between a given subset of vertices and its complement, i.e. between sides of a given partition of input vertices. Our results reveal that the ability to model interaction is primarily determined by the partition's walk index -- a graph-theoretical characteristic that we define by the number of walks originating from the boundary of the partition. Experiments with common GNN architectures corroborate this finding. As a practical application of our theory, we design an edge sparsification algorithm named Walk Index Sparsification (WIS), which preserves the ability of a GNN to model interactions when input edges are removed. WIS is simple, computationally efficient, and markedly outperforms alternative methods in terms of induced prediction accuracy. More broadly, it showcases the potential of improving GNNs by theoretically analyzing the interactions they can model.
Graph Convolutional Networks (GCNs) have been widely applied in various fields due to their significant power on processing graph-structured data. Typical GCN and its variants work under a homophily assumption (i.e., nodes with same class are prone to connect to each other), while ignoring the heterophily which exists in many real-world networks (i.e., nodes with different classes tend to form edges). Existing methods deal with heterophily by mainly aggregating higher-order neighborhoods or combing the immediate representations, which leads to noise and irrelevant information in the result. But these methods did not change the propagation mechanism which works under homophily assumption (that is a fundamental part of GCNs). This makes it difficult to distinguish the representation of nodes from different classes. To address this problem, in this paper we design a novel propagation mechanism, which can automatically change the propagation and aggregation process according to homophily or heterophily between node pairs. To adaptively learn the propagation process, we introduce two measurements of homophily degree between node pairs, which is learned based on topological and attribute information, respectively. Then we incorporate the learnable homophily degree into the graph convolution framework, which is trained in an end-to-end schema, enabling it to go beyond the assumption of homophily. More importantly, we theoretically prove that our model can constrain the similarity of representations between nodes according to their homophily degree. Experiments on seven real-world datasets demonstrate that this new approach outperforms the state-of-the-art methods under heterophily or low homophily, and gains competitive performance under homophily.
Sequential recommendation (SR) is to accurately recommend a list of items for a user based on her current accessed ones. While new-coming users continuously arrive in the real world, one crucial task is to have inductive SR that can produce embeddings of users and items without re-training. Given user-item interactions can be extremely sparse, another critical task is to have transferable SR that can transfer the knowledge derived from one domain with rich data to another domain. In this work, we aim to present the holistic SR that simultaneously accommodates conventional, inductive, and transferable settings. We propose a novel deep learning-based model, Relational Temporal Attentive Graph Neural Networks (RetaGNN), for holistic SR. The main idea of RetaGNN is three-fold. First, to have inductive and transferable capabilities, we train a relational attentive GNN on the local subgraph extracted from a user-item pair, in which the learnable weight matrices are on various relations among users, items, and attributes, rather than nodes or edges. Second, long-term and short-term temporal patterns of user preferences are encoded by a proposed sequential self-attention mechanism. Third, a relation-aware regularization term is devised for better training of RetaGNN. Experiments conducted on MovieLens, Instagram, and Book-Crossing datasets exhibit that RetaGNN can outperform state-of-the-art methods under conventional, inductive, and transferable settings. The derived attention weights also bring model explainability.
Temporal relational modeling in video is essential for human action understanding, such as action recognition and action segmentation. Although Graph Convolution Networks (GCNs) have shown promising advantages in relation reasoning on many tasks, it is still a challenge to apply graph convolution networks on long video sequences effectively. The main reason is that large number of nodes (i.e., video frames) makes GCNs hard to capture and model temporal relations in videos. To tackle this problem, in this paper, we introduce an effective GCN module, Dilated Temporal Graph Reasoning Module (DTGRM), designed to model temporal relations and dependencies between video frames at various time spans. In particular, we capture and model temporal relations via constructing multi-level dilated temporal graphs where the nodes represent frames from different moments in video. Moreover, to enhance temporal reasoning ability of the proposed model, an auxiliary self-supervised task is proposed to encourage the dilated temporal graph reasoning module to find and correct wrong temporal relations in videos. Our DTGRM model outperforms state-of-the-art action segmentation models on three challenging datasets: 50Salads, Georgia Tech Egocentric Activities (GTEA), and the Breakfast dataset. The code is available at //github.com/redwang/DTGRM.
Graph Neural Networks (GNNs) have recently become increasingly popular due to their ability to learn complex systems of relations or interactions arising in a broad spectrum of problems ranging from biology and particle physics to social networks and recommendation systems. Despite the plethora of different models for deep learning on graphs, few approaches have been proposed thus far for dealing with graphs that present some sort of dynamic nature (e.g. evolving features or connectivity over time). In this paper, we present Temporal Graph Networks (TGNs), a generic, efficient framework for deep learning on dynamic graphs represented as sequences of timed events. Thanks to a novel combination of memory modules and graph-based operators, TGNs are able to significantly outperform previous approaches being at the same time more computationally efficient. We furthermore show that several previous models for learning on dynamic graphs can be cast as specific instances of our framework. We perform a detailed ablation study of different components of our framework and devise the best configuration that achieves state-of-the-art performance on several transductive and inductive prediction tasks for dynamic graphs.
Graph Neural Networks (GNNs) have been shown to be effective models for different predictive tasks on graph-structured data. Recent work on their expressive power has focused on isomorphism tasks and countable feature spaces. We extend this theoretical framework to include continuous features - which occur regularly in real-world input domains and within the hidden layers of GNNs - and we demonstrate the requirement for multiple aggregation functions in this context. Accordingly, we propose Principal Neighbourhood Aggregation (PNA), a novel architecture combining multiple aggregators with degree-scalers (which generalize the sum aggregator). Finally, we compare the capacity of different models to capture and exploit the graph structure via a novel benchmark containing multiple tasks taken from classical graph theory, alongside existing benchmarks from real-world domains, all of which demonstrate the strength of our model. With this work, we hope to steer some of the GNN research towards new aggregation methods which we believe are essential in the search for powerful and robust models.
Graph convolution networks (GCN) are increasingly popular in many applications, yet remain notoriously hard to train over large graph datasets. They need to compute node representations recursively from their neighbors. Current GCN training algorithms suffer from either high computational costs that grow exponentially with the number of layers, or high memory usage for loading the entire graph and node embeddings. In this paper, we propose a novel efficient layer-wise training framework for GCN (L-GCN), that disentangles feature aggregation and feature transformation during training, hence greatly reducing time and memory complexities. We present theoretical analysis for L-GCN under the graph isomorphism framework, that L-GCN leads to as powerful GCNs as the more costly conventional training algorithm does, under mild conditions. We further propose L^2-GCN, which learns a controller for each layer that can automatically adjust the training epochs per layer in L-GCN. Experiments show that L-GCN is faster than state-of-the-arts by at least an order of magnitude, with a consistent of memory usage not dependent on dataset size, while maintaining comparable prediction performance. With the learned controller, L^2-GCN can further cut the training time in half. Our codes are available at //github.com/Shen-Lab/L2-GCN.
InteractE: Improving Convolution-based Knowledge Graph Embeddings by Increasing Feature Interactions
Most existing knowledge graphs suffer from incompleteness, which can be alleviated by inferring missing links based on known facts. One popular way to accomplish this is to generate low-dimensional embeddings of entities and relations, and use these to make inferences. ConvE, a recently proposed approach, applies convolutional filters on 2D reshapings of entity and relation embeddings in order to capture rich interactions between their components. However, the number of interactions that ConvE can capture is limited. In this paper, we analyze how increasing the number of these interactions affects link prediction performance, and utilize our observations to propose InteractE. InteractE is based on three key ideas -- feature permutation, a novel feature reshaping, and circular convolution. Through extensive experiments, we find that InteractE outperforms state-of-the-art convolutional link prediction baselines on FB15k-237. Further, InteractE achieves an MRR score that is 9%, 7.5%, and 23% better than ConvE on the FB15k-237, WN18RR and YAGO3-10 datasets respectively. The results validate our central hypothesis -- that increasing feature interaction is beneficial to link prediction performance. We make the source code of InteractE available to encourage reproducible research.
How can we estimate the importance of nodes in a knowledge graph (KG)? A KG is a multi-relational graph that has proven valuable for many tasks including question answering and semantic search. In this paper, we present GENI, a method for tackling the problem of estimating node importance in KGs, which enables several downstream applications such as item recommendation and resource allocation. While a number of approaches have been developed to address this problem for general graphs, they do not fully utilize information available in KGs, or lack flexibility needed to model complex relationship between entities and their importance. To address these limitations, we explore supervised machine learning algorithms. In particular, building upon recent advancement of graph neural networks (GNNs), we develop GENI, a GNN-based method designed to deal with distinctive challenges involved with predicting node importance in KGs. Our method performs an aggregation of importance scores instead of aggregating node embeddings via predicate-aware attention mechanism and flexible centrality adjustment. In our evaluation of GENI and existing methods on predicting node importance in real-world KGs with different characteristics, GENI achieves 5-17% higher NDCG@100 than the state of the art.
Graph-based semi-supervised learning (SSL) is an important learning problem where the goal is to assign labels to initially unlabeled nodes in a graph. Graph Convolutional Networks (GCNs) have recently been shown to be effective for graph-based SSL problems. GCNs inherently assume existence of pairwise relationships in the graph-structured data. However, in many real-world problems, relationships go beyond pairwise connections and hence are more complex. Hypergraphs provide a natural modeling tool to capture such complex relationships. In this work, we explore the use of GCNs for hypergraph-based SSL. In particular, we propose HyperGCN, an SSL method which uses a layer-wise propagation rule for convolutional neural networks operating directly on hypergraphs. To the best of our knowledge, this is the first principled adaptation of GCNs to hypergraphs. HyperGCN is able to encode both the hypergraph structure and hypernode features in an effective manner. Through detailed experimentation, we demonstrate HyperGCN's effectiveness at hypergraph-based SSL.
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